From Prieto-Godino LL, Rytz R, Bargeton B, Abuin L, Arguello JR, Peraro MD, Benton R, at Nature: Olfactory receptor pseudo-pseudogenes,² Nature 2016 Oct 24 doi:10.1038/nature19824. PMID:27776356 Abstract: Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. Although certain pseudogene-derived RNAs have regulatory roles, and some pseudogene fragments are translated, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species. Here we report the characterization of a pseudogene in the chemosensory variant ionotropic glutamate receptor repertoire of Drosophila sechellia, an insect endemic to the Seychelles that feeds almost exclusively on the Read More ›

From ScienceDaily: Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered “junk” because they do not code for specific proteins. … “The cardiac changes that we observed in knockout mice lacking these enhancers highlight the role of noncoding sequences in processes that are important in human disease,” said study co-senior author Axel Visel, senior staff scientist and one of three lead researchers at the Mammalian Functional Genomics Laboratory, part of Berkeley Lab’s Environmental Genomics and Systems Biology (EGSB) Division. “Identifying and interpreting sequence changes affecting noncoding sequences is increasingly a challenge in human genetics. The genome-wide catalog of heart enhancers Read More ›

From ScienceDaily: Several years ago, biologists discovered a new type of genetic material known as long noncoding RNA. This RNA does not code for proteins and is copied from sections of the genome once believed to be “junk DNA.” Since then, scientists have found evidence that long noncoding RNA, or lncRNA, plays roles in many cellular processes, including guiding cell fate during embryonic development. However, it has been unknown exactly how lncRNA exerts this influence. Inspired by historical work showing that structure plays a role in the function of other classes of RNA such as transfer RNA, MIT biologists have now deciphered the structure of one type of lncRNA and used that information to figure out how it interacts with Read More ›

From ScienceDaily: Although variants are scattered throughout the genome, scientists have largely ignored the stretches of repetitive genetic code once dismissively known as “junk” DNA in their search for differences that influence human health and disease. A new study shows that variation in these overlooked repetitive regions may also affect human health. These regions can affect the stability of the genome and the proper function of the chromosomes that package genetic material, leading to an increased risk of cancer, birth defects and infertility. The results appear online in the journal Genome Research. … “What we found in this study is probably the tip of the iceberg,” Sullivan said. “There could be all sorts of functional consequences to having variation within Read More ›

Not that you’d ever guess from the story at Scienmag, but It took nearly a half trillion tries before researchers at The University of Texas at Austin witnessed a rare event and perhaps solved an evolutionary puzzle about how introns, non-coding sequences of DNA located within genes, multiply in a genome. The results, published today in the Proceedings of the National Academy of Sciences, address fundamental questions about the evolution of new species and could expand our understanding of gene expression and the causes of diseases such as cancer. … For a long time, scientists have known that much of the DNA within any given organism’s genome does not code for functional molecules or protein. However, recent research has found that Read More ›

From ScienceDaily: What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) — genome’s messages that do not code for proteins — in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions. Yes, that’s what they said. ncRNAs come in multiple flavours: there’s rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA’s place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control Read More ›

A reader sent this link to a free 2013 paper in Genome Biol Evol wherein we read: Although once said to be “junk,” or “parasitic,” DNA (Doolittle and Sapienza 1980; Orgel and Crick 1980), a recent large and rapid accumulation of evidence indicates that transposable elements (TEs) have been a significant factor in the evolution of a wide range of eukaryotic taxa (Bennetzen 2000; Kazazian 2004; Biémont and Vieira 2006; Feschotte and Pritham 2007; Bohne et al. 2008; Hua-Van et al. 2011). We have proposed TEs as powerful facilitators of evolution (Oliver and Greene 2009), formalized this proposal into the TE-Thrust hypothesis (Oliver and Greene 2011), and more recently, expanded and strengthened this hypothesis (Oliver and Greene 2012). More. But Read More ›

Yeah, the dumpster, not the Thrift. Oh, and ID is wrong. From key proponent of junk DNA, University of Houston’s (human genome is mostly junk) Dan Graur, RUBBISH DNA: THE FUNCTIONLESS FRACTION OF THE HUMAN GENOME Abstract: Because genomes are products of natural processes rather than “intelligent design,” all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called “rubbish DNA.” Rubbish DNA consists of “junk DNA,” i.e., the fraction of the genome on which selection does not operate, and “garbage DNA,” i.e., sequences that lower the fitness of the organism, but exist in the genome because purifying selection is neither omnipotent nor instantaneous. In this chapter, I (1) review the concepts of Read More ›

Further to: Blocking “junk” DNA can prevent stroke damage (so it obviously does something, right?): In a book review in a Darwin lobby journal, “A deeper confusion,” (of The Deeper Genome and Junk DNA: A Journey Through the Dark Matter of the Genome), we read a note of concern: If taken uncritically, these texts can be expected to generate even more confusion in a field that already has a serious problem when it comes to communicating the best understanding of the science to the public. Hmmm. Anything, “taken uncritically,” can be expected to do that. So… ah, now we come to it: They will also certainly provide ammunition for intelligent design proponents and other creationists. The debunking of junk DNA and Read More ›

As we have been discussing, in 2006 Francis Collins said that Darwinism predicts (in the sense of retrodiction) that mutations located in “junk DNA” will accumulate steadily over time. A couple of years ago I said that Darwinist predictions (again, in the sense of retrodiction) about junk DNA turned out to be wrong, while ID Proponents predictions (this time in the actual sense of making an assertion about future findings) turned out to be true. It is good to know that even Collins admits this:  Earlier this year he confessed that his use of the term “junk DNA” was wrong, even hubristic.  At the 33rd Annual J.P. Morgan Healthcare Conference in San Francisco on January 13, 2015 he said: I Read More ›

From obit: Inherent in the idea of gene regulatory networks was the concept that genome sequences that provided information about how genes should be expressed would be as important as the genome sequences that coded for the proteins themselves. Although non-protein-coding DNA was long considered to be “junk,” Davidson recognized that the key regulatory code resided in this genetic material. In 2006, Davidson co-led a group of 240 researchers from more than 70 institutions that sequenced the purple sea urchin’s genome. In 2008, a consortium of institutions led by Davidson’s lab characterized the 23,000 genes of that genome. In parallel, the Davidson group systematically created a comprehensive functional testing strategy to detect all of the control connections between the genes Read More ›

From Quanta Magazine: Emerging data suggests the seemingly impossible — that mysterious new genes arise from “junk” DNA. Genes, like people, have families — lineages that stretch back through time, all the way to a founding member. That ancestor multiplied and spread, morphing a bit with each new iteration. For most of the last 40 years, scientists thought that this was the primary way new genes were born — they simply arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions. Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. They’re the Read More ›

Ken Miller is a feted Catholic scientist, friend of Darwinism, and foe of design in nature: From his 1994 textbook: Hundreds of pseudogenes have been discovered in the 1 or 2% of human DNA that has been explored to date, and more are added every month. In fact, the human genome is littered with pseudogenes, gene fragments, “orphaned” genes, “junk” DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. Read More ›

Two days ago, a big meeting in Maryland of researchers into non-coding DNA (alleged “junk DNA” ) wrapped up, and people have been writing to us about the various, so-far unofficially publicized findings that friends have told them about. One researcher whose specialty is orphan genes observed that although we have similar genes to mice, the DHS regions in the DNA associated with these genes feature only 5% similarity between mice and humans. This is all the more peculiar because the eventual development of mice is very similar to that of humans even though so many differences in regulatory pathways exist. He was part of a research team that discovered this: Abstract: To study the evolutionary dynamics of regulatory DNA, we mapped Read More ›

Peter M. Waterhouse & Roger P. Hellens, ” Plant biology: Coding in non-coding RNAs,” Nature (March 25, 2025) Dominique Lauressergues, Jean-Malo Couzigou, Hélène San Clemente, Yves Martinez, Christophe Dunand, Guillaume Bécar, & Jean-Philippe Combier, “Primary transcripts of microRNAs encode regulatory peptides,” Nature (March 25, 2015) G C S Kuhn, “‘Satellite DNA transcripts have diverse biological roles in Drosophila’,” Heredity (March 25, 2015) Go here for simple explanation. Nick Matzke? Darwin book burner! Where are you when we need you to dump on all this? You used to come at half o’clock and now you come at noon. Otherwise, Biological Information Follow UD News at Twitter!